[seek-taxon] RE: some ideas

Kennedy, Jessie J.Kennedy at napier.ac.uk
Thu Sep 18 08:16:39 PDT 2003


Hi Folks

I had a look at Dave's ideas and "think" they seem appropriate but until we
really sit down and get a common understanding it'd be hard to be sure -
they are certainly possibilities - some I like more than others. for example
idea 1. doesn't really fit with how I see things (at the moment - unless I'm
convinced otheriwse), 2. would seem sensible but we'd need to look at how we
interoperate between the SMS and TCS (taxonomic concept server)
representations; 3. Is necessary and I have thought a bit about it but agree
this would be another place where the SMS and TCS stuff should be epxlored;
4 agree with this too but have some views on where we do the cut-off of
usable names to reason about.

I think it would be very profitable to chat with Dave and think that would
be best as a group rather than individual calls - but if that's the best we
can do then so be it.

I would like to say I'll come over and meet up but I don't think it'll be
possible to meet up before Lisbon - will Dave be there? - I would hope so...

ok speak to you all soon,

Jessie 

> -----Original Message-----
> From: Beach, James H [mailto:beach at ku.edu]
> Sent: 15 September 2003 03:06
> To: Robert K. Peet
> Cc: thau at learningsite.com; Kennedy, Jessie; Bertram Ludaescher; Gauch,
> Susan Evalyn; seek-taxon at ecoinformatics.org
> Subject: RE: [seek-taxon] RE: some ideas
> 
> 
> In the SEEK NSF proposal and budget we had included a slot 
> and funding for a
> programmer who would work at the interface of the Taxon and 
> SMS groups. The
> intent was that this person would start to develop connection 
> between the
> intellectual modelling of the Taxon group and the semantic 
> architecture of
> SMS.
>  
> The thought behind hiring Dave, who has several years of 
> experience with
> semantic processing and independent experience with taxonomic 
> data, was that
> this would be an exploration in that direction.  Dave would 
> formalize some
> development objectives and scope during a 30 day contract 
> period and that we
> would as a project (Taxon, SMS, Matt) then decide whether to 
> fund his work
> plan for some additional months.  Dave would be obligated by 
> the nature of
> his role, to make sure what he proposes would have relevance 
> and eventually
> intersect the work of the two groups.  He would, as you point 
> out, not be
> working within the current scope and activities of the Taxon 
> working group,
> except to take our work as a departure and reference point 
> for some semantic
> explorations.  We discussed Thau's potential role in this 
> context during one
> of our recent Taxon teleconference calls.
>  
>  
>  
>  
> 
> -----Original Message----- 
> From: Robert K. Peet [mailto:peet at unc.edu] 
> Sent: Sun 9/14/2003 6:04 PM 
> To: Beach, James H 
> Cc: thau at learningsite.com; Kennedy, Jessie; Bertram 
> Ludaescher; Gauch, Susan
> Evalyn; seek-taxon at ecoinformatics.org 
> Subject: Re: [seek-taxon] RE: some ideas
> 
> 
> 
> 
> 
> Howdy, 
> 
> Dave Thau seems like a bright guy that we might benefit from. 
>  However, it 
> seems like he would be working in isolation from our previous 
> work.  We 
> are already working a bit too much as fragmented groups 
> rather than as a 
> coherent team.  To add another fragment would likely not be 
> productive, 
> but rather just distract us.  Is there a convenient way to 
> bring him up to 
> speed on the various things members of our group have done and then 
> interact with him regularly during the contract period so that he can 
> build on our our past work and help us to converge on a 
> common vision? 
> 
> Bob 
> 
> 
> 
> 
> On Sat, 13 Sep 2003, Beach, James H wrote: 
> 
> > 
> > Dave -- 
> > 
> > Thanks for this interesting set of ideas.  Let me forward 
> them to Matt 
> > Jones, Jessie Kennedy, Susan Gauch,  and Bertram Ludaescher 
> to see what
> they 
> > think.  I will (and maybe they will hopefully also) get 
> back to you early 
> > next week and we'll make some decisions. 
> > 
> > 
> > Jessie, Bertram, Susan and Matt --  Would you have any 
> thoughts on these 
> > suggestions from Dave Thau on possible work areas for 
> semantic processing
> of 
> > classifications.  These are just early thoughts from Dave, 
> he has not
> talked 
> > in depth with anyone of us yet. 
> > 
> > We have proposed to Dave that we would hire him as a 
> consultant on the
> SEEK 
> > Taxon group for an initial 30 day period to research the scope of
> challenges 
> > with the semantic processing of multiple classifications.  
> So this is just
> 
> > very preliminary and it would be very useful for SEEK if 
> you had any 
> > thoughts for Dave on the challenges he describes. 
> > 
> > -- Jim 
> > 
> > 
> > -------------------------------- 
> > James H. Beach 
> > Biodiversity Research Center 
> > University of Kansas 
> > 1345 Jayhawk Boulevard 
> > Lawrence, KS 66045, USA 
> > Tel: 785 864-4645, Fax: 785 864-5335 
> > Televideocon: (H.323): 129.237.201.102 
> > 
> > 
> > 
> > > -----Original Message----- 
> > > From: thau at learningsite.com [mailto:thau at learningsite.com
> <mailto:thau at learningsite.com> ] 
> > > Sent: 11 September, 2003 6:46 PM 
> > > To: Vieglais, David A; Beach, James H 
> > > Subject: some ideas 
> > > 
> > > 
> > > Howdy! 
> > > 
> > > I'd like to try out some SEEK ideas just to make sure I'm 
> > > thinking correctly.  Let me know if any of these sound 
> > > particularly interesting or particularly irrelevant.  Let me 
> > > know if I'm totally off base here too. 
> > > I haven't yet scheduled any meetings or phone calls with 
> > > anyone, so this 
> > > comes out of a bit of a vacuum. 
> > > 
> > > I've come up with four basic topics lurking around the TG/SMS 
> > > border so 
> > > far: 
> > > 
> > > 1.  Using SMS representations and languages to reason over 
> > > multiple taxonomic hierarchies. 
> > > 
> > > 2.  Using SMS to aid in building an index, registry, 
> > > collection of assertions, whatever it is that the TG will 
> be serving. 
> > > 
> > > 3.  Figuring out what to do with data sets describing taxa at 
> > > different levels (e.g. genus level data vs. species level data). 
> > > 
> > > 4.  Figuring out what to do with data sets containing 
> > > uncertain taxonomic information. 
> > > 
> > > Here are some more details about each of these.  Read on, or 
> > > if it's too much for an email, let me know if a phone call 
> > > would be more appropriate. 
> > > 
> > > 
> > > 1.  The SMS folks have various ontology representations and 
> > > inference engines.  It may be a good idea for the taxon group 
> > > to use these representations and engines when doing things 
> > > like reasoning over multiple conflicting hierarcies, or 
> > > simply responding to SMS queries.  There are a number of 
> > > things I could look into regarding that.  Some quick ideas: 
> > >   a.  working on a way for new taxonomic concept providers to 
> > > share data 
> > > with SEEK 
> > >   b.  helping translate the rules developed by the TG into 
> > > more SMS-like representations (like F-Logic and OWL) 
> > >   c.  using the SMS stuff to navigate conflicting hierarchies 
> > > - one thing to point out is that I already have a database of 
> > > conflicting taxonomic hierarchies buried in the 
> > > www.speciestoolkit.org.  Hidden in there are full > taxonomies 
> > > from species 2000, ITIS, Genbank, and a couple others. 
> > > 
> > > 2.  Using SMS to support feature extraction techniques that 
> > > may be useful in determining taxonomic concepts in EML data 
> > > sets and other types of documents. I'm a bit unclear about 
> > > what data are going to reside in a "taxanomic name server" 
> > > and what data are going to be calculated over a distributed 
> > > fashion, but assuming there's going to be some sort of index 
> > > of names or collection of assertions, or registry, SMS could 
> > > be a help in growing that index, collection or registry. 
> > > 
> > > 3.  The simple cases of SMS and TG working together are 
> > >   a.  SMS asks TG which of a set of names represent the 
> same critters 
> > >   b.  SMS gives TG as set of names and wants the accepted 
> names back 
> > >   c.  SMS wants a list of possible synonyms for some name 
> > > 
> > > However, these largely act within one level of a hierarchy. 
> > > I have some species names, I want the 'official' species 
> > > names.  What happens when SMS wants to reason over data sets 
> > > which act at different levels?  One data set may cover a 
> > > subset of a genus (e.g. Arizona desert Pheidoles) while 
> > > another might discuss a specific species (Pheidole titanus). 
> > > What role can the TG play in helping the SMS reason 
> > > accurately in cases like this? 
> > > 
> > > 4.  There seems to be a bit of confusion about what to do 
> > > with data sets which are unclear about the species they're 
> > > representing.  Those data sets may be rejected from analysis, 
> > > or perhaps the taxon group can help add a little certainty. 
> > > If a set of observations uses a common name, it may be 
> > > possible to narrow down which species they might mean using a 
> > > combination of information from that data set and some input 
> > > from the person contributing the set.  This would definitely 
> > > help the SMS in its quest to find data to contribute to an 
> > > analysis, but information generated like this should be 
> > > tagged with a certainty value of some sort. This whole area 
> > > is pretty rich for investigation. 
> > > 
> > > Ok... that's it for now.  Looking forward to your reactions. 
> > > 
> > > thau! 
> > > 
> > > 
> > > 
> > _______________________________________________ 
> > seek-taxon mailing list 
> > seek-taxon at ecoinformatics.org 
> > http://www.ecoinformatics.org/mailman/listinfo/seek-taxon
> <http://www.ecoinformatics.org/mailman/listinfo/seek-taxon>  
> > 
> 
>  ==================================================================== 
> 
>  Robert K. Peet, Professor              Phone:  919-962-6942 
>  Department of Biology, CB#3280         Fax:    919-962-6930 
>  University of North Carolina           Cell:   919-368-4971 
>  Chapel Hill, NC  27599-3280  USA       Email:  peet at unc.edu 
> 
>              http://www.bio.unc.edu/faculty/peet/
> <http://www.bio.unc.edu/faculty/peet/>  
> 
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